The first version, known as Boss Battle 1[2] or Boss Alpha Mn[3], plays during encounters with standard Alpha Metroids on the Surface, Area 1, and Area 2. This theme is very tense, relying on dissonance to create a feeling of unease. Its instrumentation consists largely of synths and other electronic instruments with Game Boy-like beats. It can be heard here: [1]

The second version of Boss Alpha, aptly named Boss Alpha2[3], plays during encounters with Evolved Alpha Metroids starting in Area 2. This theme is much more aggressive and fast-paced with a more distinct melody, but shares its style and instrumentation with Boss Battle 1. This version can be heard here: [2]

The melody of Boss Alpha2 is notably similar to the original Metroidbattle theme from Metroid II: Return of Samus, composed by Ryoji Yoshitomi. Both songs share a repeating four-note phrase, where the first two notes go down and the next two notes go up. While it lacks the opening stinger, Boss Alpha2 comes the closest to resembling the original theme when compared to other Metroid battle themes in the remake, which may have been Daisuke Matsuoka's way of incorporating the original theme.